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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag
 ||||| ||||||||  |||| ||||| |||||||| |||||||| || || ||  | ||||| ||| |||| || ||||| ||||| || |||||||||||   |      |    || |  |  |   | || | | ||| |  ||  ||||   |  | | ||  |    ||    |    | |||   ||
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaact------gatggatgtgtgtgtgttttttaaaagaaaat--atacaaaccttctctaacattgcttcttt----ttctctcctg-atag

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA01G37790.1 (Glycine max), 5'ss of exon 5
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatcttagctttcatgttcat-acaaacttgatgtaaacaggcagtgaaataacagacttgaga--taaaatactgtgcag-----
  |||| ||||||||  |||| ||||| |||||||| ||||| |||||  |||| || ||||||||||||||||| ||||| || ||||| || |||||||| |     ||       | ||   | | ||  | |  | ||| |   |||   ||| ||       ||| |  || | |  | || |  ||| | |     
TATTCTTTACTCATCAGTTGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtaccaatgcttaaaat-tgttgtttctgatacttaagagaaaatgtttgtttccagccaaaatttcaactgtattaaaatttgaacttttgttctgagaag

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G07530.1 (Glycine max), 5'ss of exon 5
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatc-ttagctttcatgttcatacaaacttgat-gtaaacaggcagtgaaataacagacttgagata--aaatactgtgcag-----
  |||| ||||||||  | || ||||| |||||||| ||||| |||||  |||| || ||||||||||||||||| ||||| || ||||| || ||||||||       ||      ||  ||   | | ||||| |  | ||  || | ||   ||| ||       ||| |  || | ||   || |  | | | |     
TATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTCTAATGCAGgtagcaatgcttaaaaaattattgtttctgatgttgaaccgaaaatgtttgtttccagccaaaatttcaactgtattaaaatgtgaacttttattctgagaag

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 4
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcc---tcatcttagctt--tcatgttcatacaaacttgatgtaaacaggcagtgaaata--acagacttgagataaaatactgtgcag-----
 ||||| ||||||||  |||| || || || ||||| ||||||||||||||||| |||||||||||||| ||||| |||||||||||| | || ||||||||  | ||  | | |    ||||||| |    ||||| |     | |  |  | ||       | | ||||   | | |  |     ||    |  |   |     
TGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTCTAATGCAGgtagtgtcatttgacataccatcttaccacaatcatgatacattacatcttttttatttttctaattaaatcttataaaaattcatcaattcgccctctcgtgtag

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ27219 (Selaginella moellendorffii), 5'ss of exon 4
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgct-ttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag
 || || ||||| ||  | ||||||||||||||||| |||||||| ||||| ||| | || |||||||  |||||| |||| ||| |||| |||||||||||  | |||| |        |  || |   | |    |      || |                                               
GGTGCTGTACTCGTCGGTCGTGTACCCCCACAACTATGGTTTCATTCCTCGTACTCTGTGCGAAGACAACGATCCATTGGACGTCTTGGTCCTGATGCAGgtagtgttctttttgtaagacgaagttactacg---gtgggggtttcag----------------------------------------------

upper sequence: AT2G18230.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ33440 (Selaginella moellendorffii), 5'ss of exon 4
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgct-ttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag
 || || ||||| ||  | ||||||||||||||||| || ||||| ||||| ||| | || |||||||  |||||| |||| ||| |||| |||||||||||  | |||| |        |  || |   | |    |      || |                                               
GGTGCTGTACTCGTCGGTCGTGTACCCCCACAACTATGGCTTCATTCCTCGTACTCTGTGCGAAGACAACGATCCATTGGACGTCTTGGTCCTGATGCAGgtagtgttctttttgtaagacgaagttactacg---gtgggggtttcag----------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116390031|gb|EG432623.1|EG432623
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|116443156|gb|EG485748.1|EG485748
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|164044854|gb|ES067559.1|ES067559
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCA
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCA
EST: gi|164017123|gb|ES146359.1|ES146359
EST:     GTAC-GATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|164064113|gb|ES130650.1|ES130650
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCA
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCA
EST: gi|116390040|gb|EG432632.1|EG432632
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|116390041|gb|EG432633.1|EG432633
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|86075558|gb|DR371315.1|DR371315
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAG                         GAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG
genomic: GAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctc ... tactgtgcagGAGCCTGTGCTAACCGGATCATTCCTCCGTGCCCGTGCTATTGGTCTAATG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTCTCTACTCATCCATTGTGTACCCCCACAACTACGGTTTCATCCCTCGAACTATCTGTGAAGACAGTGATCCAATGGATGTCCTGGTACTGATGCAGgtgctttctctcgcctcatcttagctttcatgttcatacaaacttgatgtaaacaggcagtgaaataacagacttgagataaaatactgtgcag

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